I have tried again to repoduce the bug, this time with the last version available on the github repository. It "seems" to have been fixed in version 2.39.

I say "seems" because I actually cannot build correctly dot, so the export in jpg or png is not available and graphviz/config6 file contains related errors :
#FAILS png:vrml 1
#FAILS gif:vrml 1
#FAILS jpeg:vrml 1
#FAILS jpe:vrml 1
#FAILS jpg:vrml 1
Also I've had some trouble with edgepaint binary, I had to remove "-lstdc++" from cmd/edgepaint/Makefile.in (note that I use g++-5.3, which is only available in tests repositories with Mint 17).

But in any cases, the described bug was reproductible on version 2.38 even without exporting the result to an image.